BLASTP 2.2.26 [Sep-21-2011]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= 029820
         (187 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|2D3O|1 Chain 1, Structure Of Ribosome Binding Domain Of The Trigger Factor
           On The 50s Ribosomal Subunit From D. Radiodurans
          Length = 112

 Score = 36.2 bits (82), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 31/98 (31%), Positives = 47/98 (47%), Gaps = 17/98 (17%)

Query: 40  SQDEDKIQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRREKGGKTTKVPRDFLIQILG 99
           S++ +K++ +V +      R +D+V   LAR    +PGFR        K PR  +     
Sbjct: 6   SKEGNKVEFKVSVPAAEVNRAYDQVWAGLARDV-RVPGFR------PGKAPRKVI----- 53

Query: 100 EERVTKFVVQEIVRSTL--TDYT---KKEGLNVKDKKV 132
           E RV K  V+  VR  L  T Y+   ++ GLN+ D  V
Sbjct: 54  ENRVGKGYVESQVRDRLLETHYSQGLRELGLNLVDATV 91


>pdb|2AAR|7 Chain 7, Structure Of Trigger Factor Binding Domain In Biologically
           Homologous Complex With Eubacterial Ribosome
          Length = 113

 Score = 36.2 bits (82), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 31/98 (31%), Positives = 47/98 (47%), Gaps = 17/98 (17%)

Query: 40  SQDEDKIQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRREKGGKTTKVPRDFLIQILG 99
           S++ +K++ +V +      R +D+V   LAR    +PGFR        K PR  +     
Sbjct: 5   SKEGNKVEFKVSVPAAEVNRAYDQVWAGLARDV-RVPGFR------PGKAPRKVI----- 52

Query: 100 EERVTKFVVQEIVRSTL--TDYT---KKEGLNVKDKKV 132
           E RV K  V+  VR  L  T Y+   ++ GLN+ D  V
Sbjct: 53  ENRVGKGYVESQVRDRLLETHYSQGLRELGLNLVDATV 90


>pdb|3IIV|A Chain A, Evolutionary Optimization Of Computationally Designed
           Enzymes: Kemp Eliminases Of The Ke07 Series
 pdb|3IIV|B Chain B, Evolutionary Optimization Of Computationally Designed
           Enzymes: Kemp Eliminases Of The Ke07 Series
          Length = 263

 Score = 26.9 bits (58), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 26/101 (25%), Positives = 43/101 (42%), Gaps = 3/101 (2%)

Query: 29  ITVKDAKIVVESQDEDKIQV-RVDLTGDATQRVFDKVLTNLARSAPPIPGFRREKGGKTT 87
           I ++D  + VE +   +I +  +D  G  T+  +D  +    R    +P       GKT 
Sbjct: 151 ILLRDWVVEVEKRGAGEIVLGSIDRLG--TKSGYDTEMIRFVRPLTTLPIIAHRGAGKTE 208

Query: 88  KVPRDFLIQILGEERVTKFVVQEIVRSTLTDYTKKEGLNVK 128
                FL      +  + F  +EI    L +Y KK G+NV+
Sbjct: 209 HFLEAFLAGADAAKADSVFHSREIDVRELKEYLKKHGVNVR 249


>pdb|2HQM|A Chain A, Crystal Structure Of Glutathione Reductase Glr1 From The
           Yeast Saccharomyces Cerevisiae
 pdb|2HQM|B Chain B, Crystal Structure Of Glutathione Reductase Glr1 From The
           Yeast Saccharomyces Cerevisiae
          Length = 479

 Score = 26.9 bits (58), Expect = 7.4,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 3/48 (6%)

Query: 97  ILGEERVTKFVVQEIVRSTLTDYTKKEGLNV-KDKKVTTTQKAEELRK 143
           I GE  + KF   E +++T+TD+  KEG+NV K  K+   +K  E  K
Sbjct: 215 IRGETVLRKF--DECIQNTITDHYVKEGINVHKLSKIVKVEKNVETDK 260


  Database: pdbaa
    Posted date:  Mar 3, 2013 10:34 PM
  Number of letters in database: 14,973,337
  Number of sequences in database:  62,578
  
Lambda     K      H
   0.315    0.133    0.359 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,236,649
Number of Sequences: 62578
Number of extensions: 150254
Number of successful extensions: 354
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 345
Number of HSP's gapped (non-prelim): 21
length of query: 187
length of database: 14,973,337
effective HSP length: 93
effective length of query: 94
effective length of database: 9,153,583
effective search space: 860436802
effective search space used: 860436802
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 48 (23.1 bits)